I am currently working on transcription factor binding in loops for my internship. I have just encountered a problem.
let me summarize:
In one of the side, there is a TF binding the DNA and the other side, there is a gene.
So the idea is simple: Generate a mutation in TF binding site and see if there is still a transcription of the gene in the other side.
Before to apply some mutations, I have to find 5 candidates. The problem is, I have about 1,000 candidates (for me, candidate is the loop with TF in one side, and the gene in the other side). So my idea is to select the most expressed genes among my candidates. In the end, it is to check if the TF is really involved in the transcription of the gene.
(I don't know if it is the cleanest way to process but I didn't find an other condition.)
My question is simple: Does it have a function in R or a file to have this kind of information about the gene expression.
So the type of genes is the GRange object, looks like this:
ENSG00000132196 chr1 [162790702, 162812817] + | ENSG00000132196
If you have an other solution to apply a selection among my genes, let me know.
Thank you very much,